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from random import random
from ase.ga.cutandsplicepairing import CutAndSplicePairing
from ase.ga.data import DataConnection
from ase.ga.offspring_creator import OperationSelector
from ase.ga.pbs_queue_run import PBSQueueRun
from ase.ga.population import Population
from ase.ga.standard_comparators import InteratomicDistanceComparator
from ase.ga.standardmutations import (
MirrorMutation,
PermutationMutation,
RattleMutation,
)
from ase.ga.utilities import closest_distances_generator, get_all_atom_types
from ase.io import write
def jtg(job_name, traj_file):
s = '#!/bin/sh\n'
s += '#PBS -l nodes=1:ppn=12\n'
s += '#PBS -l walltime=48:00:00\n'
s += f'#PBS -N {job_name}\n'
s += '#PBS -q q12\n'
s += 'cd $PBS_O_WORKDIR\n'
s += f'python calc.py {traj_file}\n'
return s
population_size = 20
mutation_probability = 0.3
# Initialize the different components of the GA
da = DataConnection('gadb.db')
tmp_folder = 'tmp_folder/'
# The PBS queing interface is created
pbs_run = PBSQueueRun(
da,
tmp_folder=tmp_folder,
job_prefix='Ag2Au2_opt',
n_simul=5,
job_template_generator=jtg,
)
atom_numbers_to_optimize = da.get_atom_numbers_to_optimize()
n_to_optimize = len(atom_numbers_to_optimize)
slab = da.get_slab()
all_atom_types = get_all_atom_types(slab, atom_numbers_to_optimize)
blmin = closest_distances_generator(all_atom_types, ratio_of_covalent_radii=0.7)
comp = InteratomicDistanceComparator(
n_top=n_to_optimize,
pair_cor_cum_diff=0.015,
pair_cor_max=0.7,
dE=0.02,
mic=False,
)
pairing = CutAndSplicePairing(slab, n_to_optimize, blmin)
mutations = OperationSelector(
[1.0, 1.0, 1.0],
[
MirrorMutation(blmin, n_to_optimize),
RattleMutation(blmin, n_to_optimize),
PermutationMutation(n_to_optimize),
],
)
# Relax all unrelaxed structures (e.g. the starting population)
while (
da.get_number_of_unrelaxed_candidates() > 0
and not pbs_run.enough_jobs_running()
):
a = da.get_an_unrelaxed_candidate()
pbs_run.relax(a)
# create the population
population = Population(
data_connection=da, population_size=population_size, comparator=comp
)
# Submit new candidates until enough are running
while (
not pbs_run.enough_jobs_running()
and len(population.get_current_population()) > 2
):
a1, a2 = population.get_two_candidates()
a3, desc = pairing.get_new_individual([a1, a2])
if a3 is None:
continue
da.add_unrelaxed_candidate(a3, description=desc)
if random() < mutation_probability:
a3_mut, desc = mutations.get_new_individual([a3])
if a3_mut is not None:
da.add_unrelaxed_step(a3_mut, desc)
a3 = a3_mut
pbs_run.relax(a3)
write('all_candidates.traj', da.get_all_relaxed_candidates())
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